We propose to synthesize new polyintercalators that exhibit high binding affinity and base sequence specificity for the DNA and RNA double helix. The linker connecting the intercalators is effectively a piece of organic chemistry being delivered to the groove of DNA or RNA helix. Chemical modification of any linker with regard to length, flexibility, charge, chirality, and functionality should effect the stability, kinetics, specificity, and molecular engineering capabilities of these DNA binding ligands. We suggest that intercalators are useful probes of different conformational families of DNA whose interconversion are base composition dependent. These studies on the molecular recognition of DNA and RNA by polyintercalators may provide: (1) new data for ligand/drug design with regard to the nucleic acid receptor, important in antibiotic and cancer chemotherapy; (2) new probes of nucleic acid structure, important for any molecular understanding of genetic regulation; and (3) substrates for subsequent functionalization to afford high affinity, sequence specific DNA/RNA probes capable of carrying out chemical transformations on the nucleic acid polymer.